dolfin-convert of Exodus II file

Question

Hello,

I first want to thank all of the FEniCS contributors for their great work.

As everything else works just fine, I assume this question is not related with my installation.

dolfin-convert works just fine with the .node and .ele file from the dolfin/scripts/dolfin-convert directory. The .exo however gives an error:

$:./dolfin-convert test_exodus.exo out.xml

Converting from Exodus II format to NetCDF format
Traceback (most recent call last):
  File "./dolfin-convert", line 131, in <module>
    main(sys.argv[1:])

  File "./dolfin-convert", line 78, in main
    meshconvert.convert2xml(ifilename, ofilename, iformat=iformat)

  File ".hashdist/bld/profile/d5cuhiuki6dy/lib/python2.7/site-packages/dolfin_utils/meshconvert/meshconvert.py", line 1303, in convert2xml
    convert(ifilename, XmlHandler(ofilename), iformat=iformat)

  File ".hashdist/bld/profile/d5cuhiuki6dy/lib/python2.7/site-packages/dolfin_utils/meshconvert/meshconvert.py", line 1348, in convert
    exodus2xml(ifilename, ofilename)

  File ".hashdist/bld/profile/d5cuhiuki6dy/lib/python2.7/site-packages/dolfin_utils/meshconvert/meshconvert.py", line 1287, in exodus2xml
    status, output = get_status_output('ncdump '+ifilename + ' > '+netcdffilename)

  File ".hashdist/bld/profile/d5cuhiuki6dy/lib/python2.7/site-packages/instant/output.py", line 120, in get_status_output
    pipe = Popen(cmd, shell=False, cwd=cwd, env=env, stdout=PIPE, stderr=STDOUT)

  File ".hashdist/bld/profile/d5cuhiuki6dy/lib/python2.7/subprocess.py", line 710, in __init__
    errread, errwrite)

  File ".hashdist/bld/profile/d5cuhiuki6dy/lib/python2.7/subprocess.py", line 1335, in _execute_child
    raise child_exception

OSError: [Errno 2] No such file or directory

Is this error reproducible? I'd be glad for any hints, as it seems to be a bit too deep to debug it myself within reasonable time.

Thank you very much in advance!
JonnyB

Comments

Do you get the same error if you run dolfin-convert instead of ./dolfin-convert (without ./)?

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It's trying to run ncdump, which apparently is part of netcdf. I'm guessing it cannot be reached from inside the hashdist-build..

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Ok, so you can either try to install netcdf on your system (netcdf-bin on Ubuntu) or let hashdist build and install netcdf for you.

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Thank you very much for your help. So I guess it turned out to be an installation question after all, my apologies, for using the wrong forum.

I tried to install the netcdf-bin first (Ubuntu 12.04). This solved the error above, but lead to the following error:

Converting from Exodus II format to NetCDF format
Converting from NetCDF format (.ncdf) to DOLFIN XML format
Traceback (most recent call last):
  File ".hashdist/bld/profile/sr76g7nnkasp/bin/dolfin-convert", line 131, in <module>
    main(sys.argv[1:])

  File ".hashdist/bld/profile/sr76g7nnkasp/bin/dolfin-convert", line 78, in main
    meshconvert.convert2xml(ifilename, ofilename, iformat=iformat)

  File ".hashdist/bld/profile/sr76g7nnkasp/lib/python2.7/site-packages/dolfin_utils/meshconvert/meshconvert.py", line 1303, in convert2xml
    convert(ifilename, XmlHandler(ofilename), iformat=iformat)

  File ".hashdist/bld/profile/sr76g7nnkasp/lib/python2.7/site-packages/dolfin_utils/meshconvert/meshconvert.py", line 1348, in convert
    exodus2xml(ifilename, ofilename)

  File ".hashdist/bld/profile/sr76g7nnkasp/lib/python2.7/site-packages/dolfin_utils/meshconvert/meshconvert.py", line 1291, in exodus2xml
    netcdf2xml(netcdffilename, ofilename)

  File ".hashdist/bld/profile/sr76g7nnkasp/lib/python2.7/site-packages/dolfin_utils/meshconvert/meshconvert.py", line 1174, in netcdf2xml
    ifile = open(ifilename, "r")

IOError: [Errno 2] No such file or directory: 'test_exodus.ncdf'

So I went for the hashdist build and and extend the fenics-developer-tools/install/profiles/fenics.Linux.yaml by the packages

  netcdf4:
  netcdf4cpp:
  python-netcdf4:

Unfortunately, this lead to the error (the one suggested above by Øyvind Evju?):

Converting from Exodus II format to NetCDF format
Traceback (most recent call last):
  File "./dolfin-convert", line 131, in <module>
    main(sys.argv[1:])
  File "./dolfin-convert", line 78, in main
    meshconvert.convert2xml(ifilename, ofilename, iformat=iformat)
  File ".hashdist/bld/profile/sezrvjawl7jl/lib/python2.7/site-packages/dolfin_utils/meshconvert/meshconvert.py", line 1303, in convert2xml
    convert(ifilename, XmlHandler(ofilename), iformat=iformat)
  File ".hashdist/bld/profile/sezrvjawl7jl/lib/python2.7/site-packages/dolfin_utils/meshconvert/meshconvert.py", line 1348, in convert
    exodus2xml(ifilename, ofilename)
  File ".hashdist/bld/profile/sezrvjawl7jl/lib/python2.7/site-packages/dolfin_utils/meshconvert/meshconvert.py", line 1289, in exodus2xml
    raise IOError("Something wrong while executing ncdump. Is ncdump "\
IOError: Something wrong while executing ncdump. Is ncdump installed on the system?

Am I missing another package? Any suggestions appreciated. Thanks!

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Ok, the netcdf-bin Ubuntu package will not work with the HashDist build since they have different versions of HDF5.

On the other hand, adding netcdf4: in fenics-developer-tools/install/profiles/fenics.Linux.yaml works fine for me. Just run

cd fenics-developer-tools
./install/fenics-install.sh install/profiles/fenics.Linux.yaml

Then run source fenics.custom when it has finished and ncdump should be in your path.

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Mhm, that's what I did. I also tried on another machine today. Same issue.

I'm giving up now and look for a workaround. I basically just wanted to have a "connection" to all the mesh formats supported by vtk, and I read that it's the recommended way to go across the Exodus II format. But I guess, a little script that writes the dolfin xml files directly will also do it.

Thanks for your help anyway!